"Some areas are difficult to access and people are trapped there. Rivers are overflowing, dams [are] breaking and the main roads can't be used," reports Fr George Sigamoney, Secretary General of Caritas Sri Lanka.
More than one million people have been affected in the worst hit districts of Batticaloa, Trincomalee and Amparai in the east, but rains have also caused problems in the north and central regions of the country.
The UN estimates that 390,000 people have been forced to flee their homes, while at least 37 people have been killed.
The torrential rain is already starting to undo some of the progress made in the country's recovery since the end of war.
"In the north east hundreds of farmers had started to cultivate their fields again after the war. But these efforts are turning to be futile as the rains continue to lash the rice growing areas," explained Fr Sigamoney.
"A lot of houses from our shelter programmes have been damaged in the floods as well."
The aid agency warned that even some of the temporary camps set up for flood victims had been deluged.
It has launched an appeal to help send food packages containing rice, flour, sugar soap and other essential items to victims, while around 850 displaced families are to receive shelter materials.
Christian Aid has listed Sri Lanka as one of its areas of concern. It has allocated £50,000 to partner OfERR, which is planning to distribute food, bedding, clothing, and other essentials to 25,000 people.
World Vision said that with no sign of a halt to the rains, even more people were expected to need help in the coming days.
"This is one of the worst natural disasters to hit the country in recent times," said Suresh Bartlett, World Vision Sri Lanka's National Director.
"There is devastation everywhere, many communities have lost their livelihoods and are desperately in need of food, water and other relief items."
Christian Aid has also designated the Philippines an area of concern. Flooding in recent weeks has killed more than 40 people and affected an estimated one million. It has allocated £50,000 to provide food, cooking utensils, personal hygiene kits and medicines to those affected.
In Brazil, more than 500 people have been killed by torrential rains that have triggered floods and mudslides that have in some places washed away entire neighbourhoods.
The Bishop of Petropolis told the Secretary General of Caritas Brazil, Maria Cristina dos Anjos, that there was "total chaos" in his area.
"People urgently need drinking water, food and hygiene articles. Many have lost their homes," said Ms dos Anjos.
Local churches have opened their doors to shelter some of the people made homeless by landslides. She said more needed to be done to improve the living conditions of poor people in Brazil.
"As usual, the poorest are the worst affected in this disaster," continued Ms dos Anjos. "Those who live in makeshift homes and who out of poverty have to settle in high risk zones are particularly vulnerable. More prevention could have saved many lives in this disaster."